GCR131

Overview
NameGCR131
Smed IDSMED30009966
Length (bp)953
Neoblast Clusters

Zeng et. al., 2018



 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30009966

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testisSMED30009966SMESG000061085.1 GCR131smed_ncbi_20200123PMID:27163480
Saberi et al., 2016		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of GCR131 vs. TrEMBL
Match: A0A193KUM5 (GCR131 OS=Schmidtea mediterranea OX=79327 GN=gcr131 PE=2 SV=1)

HSP 1 Score: 491.5 bits (1264), Expect = 5.948e-174
Identity = 265/265 (100.00%), Postives = 265/265 (100.00%), Query Frame = 3 
Query:   54 MFFLSIGGIVSMFFVIILCNKVKFIYFIIGSLFCSAGICLFGVLATSILFIEQENFAIQLGIFALIVELSRFACISFIRFIVKYLLDDYVISNKRGDIRTDVHYFDKGMMKKAPIINIKEVAFSTGMGFAISVXXXXXXXXXXXXXXXSQNNFVLFKGLHYTMMSWLHILWMIISFIGYDEQKYYYHMIIAVIHAIQLQIAQSNVVEGFLHQITLVIGDLIVLLISIIWTLYLLDMVLFNYFASWRLKKHISSNIIYSDKSFTSL 848
            MFFLSIGGIVSMFFVIILCNKVKFIYFIIGSLFCSAGICLFGVLATSILFIEQENFAIQLGIFALIVELSRFACISFIRFIVKYLLDDYVISNKRGDIRTDVHYFDKGMMKKAPIINIKEVAFSTGMGFAISVSFFLILDFMFILDSISQNNFVLFKGLHYTMMSWLHILWMIISFIGYDEQKYYYHMIIAVIHAIQLQIAQSNVVEGFLHQITLVIGDLIVLLISIIWTLYLLDMVLFNYFASWRLKKHISSNIIYSDKSFTSL
Sbjct:    1 MFFLSIGGIVSMFFVIILCNKVKFIYFIIGSLFCSAGICLFGVLATSILFIEQENFAIQLGIFALIVELSRFACISFIRFIVKYLLDDYVISNKRGDIRTDVHYFDKGMMKKAPIINIKEVAFSTGMGFAISVSFFLILDFMFILDSISQNNFVLFKGLHYTMMSWLHILWMIISFIGYDEQKYYYHMIIAVIHAIQLQIAQSNVVEGFLHQITLVIGDLIVLLISIIWTLYLLDMVLFNYFASWRLKKHISSNIIYSDKSFTSL 265
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BLAST of GCR131 vs. Planmine SMEST
Match: SMESG000061085.1 (SMESG000061085.1)

HSP 1 Score: 426.787 bits (1096), Expect = 5.597e-152
Identity = 232/233 (99.57%), Postives = 232/233 (99.57%), Query Frame = 3 
Query:  153 CS-AGICLFGVLATSILFIEQENFAIQLGIFALIVELSRFACISFIRFIVKYLLDDYVISNKRGDIRTDVHYFDKGMMKKAPIINIKEVAFSTGMGFAISVXXXXXXXXXXXXXXXSQNNFVLFKGLHYTMMSWLHILWMIISFIGYDEQKYYYHMIIAVIHAIQLQIAQSNVVEGFLHQITLVIGDLIVLLISIIWTLYLLDMVLFNYFASWRLKKHISSNIIYSDKSFTSL 848
            CS AGICLFGVLATSILFIEQENFAIQLGIFALIVELSRFACISFIRFIVKYLLDDYVISNKRGDIRTDVHYFDKGMMKKAPIINIKEVAFSTGMGFAISVSFFLILDFMFILDSISQNNFVLFKGLHYTMMSWLHILWMIISFIGYDEQKYYYHMIIAVIHAIQLQIAQSNVVEGFLHQITLVIGDLIVLLISIIWTLYLLDMVLFNYFASWRLKKHISSNIIYSDKSFTSL
Sbjct:   30 CSTAGICLFGVLATSILFIEQENFAIQLGIFALIVELSRFACISFIRFIVKYLLDDYVISNKRGDIRTDVHYFDKGMMKKAPIINIKEVAFSTGMGFAISVSFFLILDFMFILDSISQNNFVLFKGLHYTMMSWLHILWMIISFIGYDEQKYYYHMIIAVIHAIQLQIAQSNVVEGFLHQITLVIGDLIVLLISIIWTLYLLDMVLFNYFASWRLKKHISSNIIYSDKSFTSL 262
The following BLAST results are available for this feature:
BLAST of GCR131 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A193KUM55.948e-174100.00GCR131 OS=Schmidtea mediterranea OX=79327 GN=gcr13... [more]
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BLAST of GCR131 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of GCR131 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000061085.15.597e-15299.57SMESG000061085.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009966 ID=SMED30009966|Name=GCR131|organism=Schmidtea mediterranea sexual|type=transcript|length=953bp
GGATTTTTATGAATTATAATCGTTTAACGTAAAAAGCAAAGAAAAGGTTT
AAAATGTTTTTTCTATCAATTGGAGGAATAGTTTCGATGTTTTTTGTTAT
TATATTATGCAACAAAGTGAAATTCATATATTTTATAATTGGAAGCCTTT
TTTGTTCAGCTGGAATTTGCTTATTTGGAGTTCTTGCTACTAGTATTTTA
TTCATAGAACAAGAAAATTTTGCCATTCAACTTGGAATATTTGCATTGAT
CGTTGAACTTAGCAGATTTGCTTGCATTTCATTTATTAGGTTCATAGTGA
AATATCTTTTGGATGATTATGTTATATCTAATAAGCGAGGCGACATTCGG
ACAGATGTTCATTACTTTGATAAAGGAATGATGAAAAAAGCTCCGATTAT
AAATATAAAAGAAGTGGCTTTCAGCACTGGAATGGGTTTTGCCATAAGTG
TTTCATTCTTTCTTATTTTAGATTTTATGTTCATTTTGGATTCGATTTCT
CAAAATAATTTTGTTCTTTTCAAAGGCTTGCACTATACGATGATGTCATG
GCTCCATATCCTGTGGATGATCATTTCATTTATTGGTTATGATGAACAAA
AATATTATTATCATATGATAATAGCAGTAATTCATGCTATACAGTTACAA
ATAGCCCAATCTAATGTTGTAGAGGGCTTTTTACATCAAATAACTCTGGT
TATTGGAGATTTAATTGTTTTACTAATTAGTATTATTTGGACCCTGTACT
TACTGGACATGGTTTTATTTAATTACTTCGCTTCGTGGCGATTAAAAAAG
CACATTTCGAGTAACATTATTTACAGTGATAAATCTTTTACCAGCCTCTA
AAAACCATATTTTTGTTTGAAATAACAGCACTGATATTATTCATATTTTA
TTTTAAACAAAAGTTTTATGCAAAATTCTTACTTGTTAACTCACAAACTT
AAC
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protein sequence of SMED30009966-orf-1

>SMED30009966-orf-1 ID=SMED30009966-orf-1|Name=SMED30009966-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=266bp
MFFLSIGGIVSMFFVIILCNKVKFIYFIIGSLFCSAGICLFGVLATSILF
IEQENFAIQLGIFALIVELSRFACISFIRFIVKYLLDDYVISNKRGDIRT
DVHYFDKGMMKKAPIINIKEVAFSTGMGFAISVSFFLILDFMFILDSISQ
NNFVLFKGLHYTMMSWLHILWMIISFIGYDEQKYYYHMIIAVIHAIQLQI
AQSNVVEGFLHQITLVIGDLIVLLISIIWTLYLLDMVLFNYFASWRLKKH
ISSNIIYSDKSFTSL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
Vocabulary: INTERPRO
TermDefinition
IPR009294Aph-1
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
GO:0016020membrane
Vocabulary: biological process
TermDefinition
GO:0043085positive regulation of catalytic activity
GO:0016485protein processing
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR009294Gamma-secretase subunit Aph-1PFAMPF06105Aph-1coord: 2..234
e-value: 1.7E-8
score: 34.2
NoneNo IPR availableTMHMMTMhelixcoord: 29..51
NoneNo IPR availableTMHMMTMhelixcoord: 4..22
NoneNo IPR availableTMHMMTMhelixcoord: 56..78
NoneNo IPR availableTMHMMTMhelixcoord: 221..243
NoneNo IPR availableTMHMMTMhelixcoord: 184..201
NoneNo IPR availableTMHMMTMhelixcoord: 158..177
NoneNo IPR availableTMHMMTMhelixcoord: 121..143